# HG changeset patch
# User in_silico
# Date 1500490143 14400
# Node ID 6b7ce75ea2f863bd12c3d5c892d10ace00248a1f
# Parent  27c0b0f841c85bc46d4a8f90c075857b178a91eb
Uploaded

diff -r 27c0b0f841c8 -r 6b7ce75ea2f8 cravat_annotate_mutations-18ce5c6169ef/cravat_annotate.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_annotate_mutations-18ce5c6169ef/cravat_annotate.py	Wed Jul 19 14:49:03 2017 -0400
@@ -0,0 +1,83 @@
+import requests
+import json
+import sys
+from __builtin__ import False
+#Gets the input and output from galaxy
+input_filename = sys.argv[1]
+output_filename = sys.argv[2]
+
+#opens each file, in to read, out to write
+in_file = open(input_filename, "r")
+out_file = open(output_filename, "w")
+
+
+#sets replacements to replace each space in genomic coordinates with an underscore to run with the query
+replacements = {' ':'_'}
+#so we only print out the Keys once
+write_header = True 
+
+#loops through the input file line by line
+for line in in_file:
+    #strips the input line of \n (new line) and replaces every space with an underscore   
+    line = "_".join( line.split() )
+    #gets request from CRAVAT server with the inputed mutation line
+    call = requests.get('http://staging.cravat.us/CRAVAT/rest/service/query', params={'mutation': line} )
+    #puts the string of data into a json dictionary
+    json_data = json.loads(call.text)
+    #manually sets the order of the Keys to the same as CRAVAT Server
+    keys = ["Chromosome","Position","Strand","Reference base(s)","Alternate base(s)","HUGO symbol",
+            "Sequence ontology transcript","Sequence ontology protein change","Sequence ontology",
+            "Sequence ontology all transcripts","ExAC total allele frequency",
+            "ExAC allele frequency (African/African American)","ExAC allele frequency (Latino)",
+            "ExAC allele frequency (East Asian)","ExAC allele frequency (Finnish)",
+            "ExAC allele frequency (Non-Finnish European)","ExAC allele frequency (Other)",
+            "ExAC allele frequency (South Asian)", "1000 Genomes allele frequency",
+            "ESP6500 allele frequency (European American)","ESP6500 allele frequency (African American)",
+            "Transcript in COSMIC","Protein sequence change in COSMIC",
+            "Occurrences in COSMIC [exact nucleotide change]","Mappability Warning","Driver Genes",
+            "TARGET","dbSNP","MuPIT Link"]
+    print json_data
+    
+    #Spit out first 8 or 9, then loop through rest and print out
+    for key in json_data:
+        if key not in keys:
+            keys.append(key)
+    
+    #used so we only print out the Keys once
+    if write_header == True:
+        #writes out the keys of the dictionary
+        out_file.write('\t'.join(keys) + '\n')
+        write_header = False
+        
+    #sets value to the first value in the first key
+    value = json_data[keys[0]]
+    #actually writes out the value
+    out_file.write(value)
+    #print "key[" + key[0] + "] value[" + str(value) + "]"
+    #sets value to the second key
+    value = json_data[keys[1]]
+    out_file.write('\t' + value)
+    #print "key[" + key[1] + "] value[" + str(value) + "]"
+    
+    
+    #loops through all other values for each key
+    for key in keys[2:]:
+        #strips the value
+        value = json_data[key].strip()
+        #another try, except statement to convert the rest of the values to floats, and then round them to four decimals
+        try:
+            value = float(value)
+            value = '%.4f'%value
+        except:
+            pass
+        #writes out the value with a tab after for galaxy formatting 
+        out_file.write("\t" + str(value))
+        #print for debugging
+        print "key[" + key + "] value[" + str(value) + "]"
+    #creates a new line for the next set of values
+    out_file.write('\n')
+    
+
+#closes both files    
+in_file.close()
+out_file.close()